Have a virtual harddisk (100GB) that the properties says it is under 10GB free but when computing files and folders the free size is 60GB. After re-starting the server the properties shows the correct amount 60GB free again. This has happened twice within 2-3 months time frame. Somenone have any ideas what can cause this strange behavior of our virtual windows 2003 server? It is used as a fileserver and the Citrix Xenserver contains 4 virual harddisks (which 3 are win2003) but only the one acting as a fileserver has this problem.

Shadow copies can definitely be a reason. Also, if this VM is a file server there may be temporary cached data on the server side of the shares. These would not show up as "files" because they are state data. If this only happens on the fileserver and not the other VMs, my guess is you have to investigate that service.

You may want to check the cache settings on the server (and clients?). If this takes 2-3 months to occur, you probably have a "memory leak" with a caching process.